In recent years, rare earth-doped upconversion (UC) micro/nanocrystals are useful for many applications, especially in biology because of their unique luminescent properties and specific geometry. The luminescence efficiency of lanthanide-doped UC nanoparticles is of particular importance for their applications. However, the unsatisfactory UC efficiency is still one of the main hurdles. In the present article, a series of Yb3+/Er3+ doped NaYF4 micro/nanoparticles with different ratios of length to diameter are successfully synthesized by a facile hydrothermal route. X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy (EDX) analyses, photoluminescence spectra, and the dynamic process of the luminescence are used to characterize the samples. The intrinsic structural feature of fluoride, the solution pH value, and organic additive Cit3- account for the ultimate shape evolution of the final products. The ratio of length to diameter of NaYF4 microrod can be tuned only by varying the value of pH or the amount of an organic additive (Cit3-). The UC characteristics of a single NaYF4:Yb3+/Er3+ microrod obtained by tuning the value of pH or the amount of Cit3- are investigated by laser confocal microscopy with a 980 nm laser. The two series of codoped fluoride crystals both exhibit the characteristic UC luminescence from Er3+ ions and display the rich luminescence patterns in space. The UC luminescence from a single NaYF4:Yb3+/Er3+ microrod obtained by tuning the value of pH is brighter than that from a single NaYF4:Yb3+/Er3+ microrod with the same size obtained by tuning the amount of Cit3-. The EDX analysis indicates that the number of Na+ defects depends on the specific synthesis conditions of the sample. The Na+ defects of samples obtained by tuning the values of pH are lower than those of samples with the same size obtained by tuning the amount of Cit3-. It conduces to reducing Na+ defects at lower pH value. The parameters of the luminescence kinetics are found to be unambiguously dependent on the size of sample, which relates to higher energy phonon of surface and Na+ defects. The mechanism of luminescence enhancement by pH controlling is explored, and a mechanism based on the reduced intrinsic defects of Na+ is proposed. The investigation not only enriches the controllable synthesis approach of fluoride micro/nanomaterials, but also indicates the potential applications of rare earth materials with a rich luminescence pattern in the photonic devices and anti-counterfeiting devices.